MiniSeq / iSeq
The file structure for a miniseq / iseq run should be correct by default, but if you are having problems uploading, please verify your file structure is correct.
. ├── CompletedJobInfo.xml ├── Alignment_1 │ └── <DateTimeFolder> │ └── Fastq │ ├── sample1_S1_L001_R1_001.fastq.gz │ ├── sample1_S1_L001_R2_001.fastq.gz │ ├── sample2_S1_L001_R1_001.fastq.gz │ ├── sample2_S1_L001_R2_001.fastq.gz │ ├── sample3_S1_L001_R1_001.fastq.gz │ ├── sample3_S1_L001_R2_001.fastq.gz │ └── <other files> ├── SampleSheet.csv └── <other files>
Example files can be found:
Preparing your miniseq / iseq sample sheet
Before using the uploader, you must prepare your sequencing run with IRIDA-specific project IDs. You must do this manually after a run completes by editing
SampleSheet.csv with Microsoft Excel or Windows Notepad.
Simply add the
Sample_Project column to the
[Data] header, and add the IRIDA project number.
An example, completed miniseq
SampleSheet.csv with the
Sample_Project column filled in looks like:
[Header] Local Run Manager Analysis Id,3003 Date,10/27/2018 Experiment Name,20181026-MiniSeqTest Workflow,GenerateFastQWorkflow Description,Auto generated sample sheet. Used by workflow module to kick off Isis analysis Chemistry,Amplicon [Reads] 251 251 [Settings] Adapter,ATCGATCGATCG [Data] Sample_ID,Sample_Name,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project sample1-3003,sample1,ATCGAAA,N801,ATCGAAA,S801,1 sample2-3003,sample2,ATCGAAA,N801,ATCGAAA,S801,1 sample3-3003,sample3,ATCGAAA,N801,ATCGAAA,S801,1
Note: An iseq run will look almost the same, but a
Description field under
[DATA] may also be present. This is expected and the parser should function normally with the field there.